Merge branch 'develop' into update_212_Dec_merge_with_21125_chamges

[jalview.git] / src / jalview / gui / PopupMenu.java

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index ff70162..3c32180 100644 (file)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -20,6 +20,8 @@
  */
 package jalview.gui;
 
+import java.util.Locale;
+
 import java.awt.BorderLayout;
 import java.awt.Color;
 import java.awt.event.ActionEvent;
@@ -54,7 +56,7 @@ import jalview.analysis.AlignmentAnnotationUtils;
 import jalview.analysis.AlignmentUtils;
 import jalview.analysis.Conservation;
 import jalview.api.AlignViewportI;
-import jalview.bin.Cache;
+import jalview.bin.Console;
 import jalview.commands.ChangeCaseCommand;
 import jalview.commands.EditCommand;
 import jalview.commands.EditCommand.Action;
@@ -64,11 +66,13 @@ import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.MappedFeatures;
 import jalview.datamodel.PDBEntry;
+import jalview.datamodel.ResidueCount;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.gui.ColourMenuHelper.ColourChangeListener;
 import jalview.gui.JalviewColourChooser.ColourChooserListener;
+import jalview.io.CountReader;
 import jalview.io.FileFormatI;
 import jalview.io.FileFormats;
 import jalview.io.FormatAdapter;
@@ -87,6 +91,8 @@ import jalview.util.StringUtils;
 import jalview.util.UrlLink;
 import jalview.viewmodel.seqfeatures.FeatureRendererModel;
 
+import java.io.IOException;
+import java.net.MalformedURLException;
 /**
  * The popup menu that is displayed on right-click on a sequence id, or in the
  * sequence alignment.
@@ -228,13 +234,13 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
         urlLink = new UrlLink(link);
       } catch (Exception foo)
       {
-        Cache.log.error("Exception for URLLink '" + link + "'", foo);
+        Console.error("Exception for URLLink '" + link + "'", foo);
         continue;
       }
 
       if (!urlLink.isValid())
       {
-        Cache.log.error(urlLink.getInvalidMessage());
+        Console.error(urlLink.getInvalidMessage());
         continue;
       }
 
@@ -545,6 +551,35 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
         }
       }
 
+      if (seq.hasHMMProfile())
+      {
+        menuItem = new JMenuItem(MessageManager
+                .getString("action.add_background_frequencies"));
+        menuItem.addActionListener(new ActionListener()
+        {
+          @Override
+          public void actionPerformed(ActionEvent e)
+          {
+            try
+            {
+              ResidueCount counts = CountReader.getBackgroundFrequencies(ap,
+                      seq);
+              if (counts != null)
+              {
+                seq.getHMM().setBackgroundFrequencies(counts);
+                ap.alignFrame.buildColourMenu();
+              }
+            } catch (MalformedURLException e1)
+            {
+              e1.printStackTrace();
+            } catch (IOException e1)
+            {
+              e1.printStackTrace();
+            }
+          }
+        });
+        add(menuItem);
+      }
       menuItem = new JMenuItem(
               MessageManager.getString("action.hide_sequences"));
       menuItem.addActionListener(new ActionListener()
@@ -668,8 +703,10 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
       {
         buildGroupURLMenu(sg, groupLinks);
       }
+      // TODO REMOVE FOR 2.12 ?
       // Add a 'show all structures' for the current selection
-      Hashtable<String, PDBEntry> pdbe = new Hashtable<>(), reppdb = new Hashtable<>();
+      Hashtable<String, PDBEntry> pdbe = new Hashtable<>();
+      Hashtable<String, PDBEntry> reppdb = new Hashtable<>();
 
       SequenceI sqass = null;
       for (SequenceI sq : alignPanel.av.getSequenceSelection())
@@ -837,10 +874,14 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
       /*
        * show local rather than linked feature coordinates
        */
-      int[] beginRange = mf.getMappedPositions(start, start);
-      start = beginRange[0];
-      int[] endRange = mf.getMappedPositions(end, end);
-      end = endRange[endRange.length - 1];
+      int[] localRange = mf.getMappedPositions(start, end);
+      if (localRange == null)
+      {
+        // e.g. variant extending to stop codon so not mappable
+        return;
+      }
+      start = localRange[0];
+      end = localRange[localRange.length - 1];
     }
     StringBuilder desc = new StringBuilder();
     desc.append(sf.getType()).append(" ").append(String.valueOf(start));
@@ -1125,7 +1166,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
         for (int d = 0; d < nd; d++)
         {
           DBRefEntry e = dbr.get(d);
-          String src = e.getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase();
+          String src = e.getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase(Locale.ROOT);
           Object[] sarray = commonDbrefs.get(src);
           if (sarray == null)
           {
@@ -1159,19 +1200,19 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
         urlLink = new GroupUrlLink(link);
       } catch (Exception foo)
       {
-        Cache.log.error("Exception for GroupURLLink '" + link + "'", foo);
+        Console.error("Exception for GroupURLLink '" + link + "'", foo);
         continue;
       }
       if (!urlLink.isValid())
       {
-        Cache.log.error(urlLink.getInvalidMessage());
+        Console.error(urlLink.getInvalidMessage());
         continue;
       }
       final String label = urlLink.getLabel();
       boolean usingNames = false;
       // Now see which parts of the group apply for this URL
       String ltarget = urlLink.getTarget(); // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());
-      Object[] idset = commonDbrefs.get(ltarget.toUpperCase());
+      Object[] idset = commonDbrefs.get(ltarget.toUpperCase(Locale.ROOT));
       String[] seqstr, ids; // input to makeUrl
       if (idset != null)
       {
@@ -1807,7 +1848,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
       contents.append("<p><h2>" + MessageManager.formatMessage(
               "label.create_sequence_details_report_annotation_for",
               new Object[]
-              { seq.getDisplayId(true) }) + "</h2></p><p>");
+              { seq.getDisplayId(true) }) + "</h2></p>\n<p>");
       new SequenceAnnotationReport(false).createSequenceAnnotationReport(
               contents, seq, true, true, ap.getSeqPanel().seqCanvas.fr);
       contents.append("</p>");
@@ -2040,8 +2081,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
                   ap.paintAlignment(false, false);
                 }
                 sequence.setDescription(dialog.getDescription());
-                ap.av.firePropertyChange("alignment", null,
-                        ap.av.getAlignment().getSequences());
+                ap.av.notifyAlignment();
               }
             });
   }
@@ -2172,9 +2212,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
               startEnd, caseChange);
 
       ap.alignFrame.addHistoryItem(caseCommand);
+      ap.av.notifyAlignment();
 
-      ap.av.firePropertyChange("alignment", null,
-              ap.av.getAlignment().getSequences());
 
     }
   }
@@ -2281,8 +2320,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
                           sg.getStartRes(), sg.getEndRes() + 1,
                           ap.av.getAlignment());
                   ap.alignFrame.addHistoryItem(editCommand);
-                  ap.av.firePropertyChange("alignment", null,
-                          ap.av.getAlignment().getSequences());
+                  ap.av.notifyAlignment();
                 }
               });
     }